g_hydorder(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_hydorder(1)
NAME
g_hydorder - computes tetrahedrality parameters around a given atom VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_hydorder -f traj.xtc -n index.ndx -s topol.tpr -o intf.xpm -or raw.out -Spect intfspect.out -[no]h -[no]version -nice int -b time -e time
-dt time -[no]w -d enum -bw real -sgang1 real -sgang2 real -tblock int -nlevel int
DESCRIPTION
The tetrahedrality order parameters can be determined around an atom. Both angle an distance order parameters are calculated. See P.-L.
Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518. for more details. This application calculates the orderparameter in a 3d-mesh in
the box, and with 2 phases in the box gives the user the option to define a 2D interface in time separating the faces by specifying parame-
ters -sgang1 and -sgang2 (It is important to select these judiciously)
FILES
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-n index.ndx Input
Index file
-s topol.tpr Input
Run input file: tpr tpb tpa
-o intf.xpm Output, Mult.
X PixMap compatible matrix file
-or raw.out Output, Opt., Mult.
Generic output file
-Spect intfspect.out Output, Opt., Mult.
Generic output file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 19
Set the nicelevel
-b time 0
First frame (ps) to read from trajectory
-e time 0
Last frame (ps) to read from trajectory
-dt time 0
Only use frame when t MOD dt = first time (ps)
-[no]wno
View output .xvg, .xpm, .eps and .pdb files
-d enum z
Direction of the normal on the membrane: z, x or y
-bw real 1
Binwidth of box mesh
-sgang1 real 1
tetrahedral angle parameter in Phase 1 (bulk)
-sgang2 real 1
tetrahedral angle parameter in Phase 2 (bulk)
-tblock int 1
Number of frames in one time-block average
-nlevel int 100
Number of Height levels in 2D - XPixMaps
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_hydorder(1)